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A genetic multicolor cell-labeling technique for Droshophila melanogaster, Flybow, is described and applied to the study of neural circuits. This method implements a variant of the mouse Brainbow strategy in combination with specific neuronal targeting using the Gal-4–upstream activating sequence system to select for membrane-tethered fluorescent proteins. Also in this issue, Hampel et al. report a similar strategy, Drosophila Brainbow, to select for epitope-tagged proteins detectable via immunofluorescence.
A genetic multicolor cell-labeling technique for Droshophila melanogaster, Drosophila Brainbow, is described and applied to the study of neural circuits. This method implements a variant of the mouse Brainbow strategy in combination with specific neuronal targeting using the Gal-4–upstream activating sequence system to select for epitope-tagged proteins detectable with immunofluorescence. Also in this issue, Hadjieconomou et al. develop a similar strategy, Flybow, to select for membrane-tethered fluorescent proteins.
By methylating the phosphate groups of PtdIns(3,4,5)P3 researchers can load this lipid more efficiently into a mass spectrometer and thus this lipid can be quantified in the presence of an internal synthetic standard.
An optogenetic illumination system based on the use of a digital micromirror device and video tracking software is reported, which allows real-time light delivery with high spatial resolution to specified targets in freely moving Caenorhabditis elegans. Also in this issue, Stirman et al. report a similar illumination system using a liquid crystal display projector. Both methods allow optogenetic perturbation of a variety of neural circuits in the behaving worm.
An optogenetic illumination system based on the use of a liquid crystal display projector and video tracking software is reported, which allows real-time multispectral light delivery with high spatial resolution to specified targets in freely moving Caenorhabditis elegans. Also in this issue, Leifer et al. report a similar illumination system using a digital micromirror device. Both methods allow optogenetic perturbation of a variety of neural circuits in the behaving worm.
By individually replacing 16 yeast genes encoding ABC transporters by GFP, mating and selecting for strains with accumulated mutations the authors create a Green Monster, a strain with deletions in all 16 genes.
A microfluidic embryo-trap array for large-scale end-on imaging of Drosophila melanogaster embryos permits quantitative analysis of dorsoventral gradients during development.
The Network-Free Stochastic Simulator (NFsim) allows the representation of complex biological systems as rule-based models and facilitates coarse-graining of the reaction mechanisms.
Fast, two-photon intravital imaging of a mechanically stabilized and physiologically intact preparation of the mouse lung is reported. It is used to monitor immune cells in the lung under normal and injured conditions.
Derivatizing glycosphingolipids, extracted from bovine brain or human erythrocytes, with a fluorescent tag allows their immobilization on an array which can be probed with glycan binding proteins.
Identification of residues critical for dimerization of the Fok1 nuclease domain of zinc-finger nucleases permits rational design of enzymes with improved cleavage activity and retained obligate heterodimerization. Also in this issue, Sander et al. report context-dependent assembly (CoDA), a simple method for designing zinc-finger nucleases.
Methods are reported for the combination of fluorescence nanoscopy using either stimulated emission depletion microscopy (STED) or photoactivated localization microscopy (PALM) with electron microscopy, to achieve correlative imaging in which the super-resolved fluorescence signal is placed in the context of cellular ultrastructure.
Defined surfaces displaying heparin-binding peptides support long-term culture of multiple human embryonic and induced pluripotent stem cell lines in defined media.
A statistical approach to quantitatively derive single and double mutant fitness from colony-based growth assays is described. The resultant SGA score permits assessment of yeast fitness and genetic interactions on the genome scale.
The mixture of isoforms model (MISO) assesses the confidence in estimates of the abundance of spliced exons or isoforms from paired-end RNA-seq data and detects their differential expression.
High-throughput sequencing of RNA fragments generated from a single-strand RNA-specific nuclease followed by novel computational analysis yields structural insights into noncoding RNA at the transcriptome level.
Readily synthesized maltose–neopentyl glycol (MNG) amphiphiles are useful reagents for stabilizing, extracting and crystallizing a variety of integral membrane proteins and have favorable properties relative to conventional detergents.
Retroviral integration is used to mark clones in human embryonic stem cell cultures and clonal distribution is assessed after functionally testing the cells with different methods. Distinct subsets of clones are detected after in vitro differentiation versus teratoma formation in vivo.
Proteins can be transferred between cells in contact, such as via trogocytosis in lymphocytes, or acquired via bacteria-host interactions during infection. A quantitative proteomics approach to identify such non-cell-autonomous proteins is described.
